2025
Rates of Evolution of Developmental Changes in Gene Expression in Sordariomycetes
Wang Y, Wang F, Meng G, Lopez-Giraldez F, Dong C, Wang Z, Townsend J. Rates of Evolution of Developmental Changes in Gene Expression in Sordariomycetes. Molecular Biology And Evolution 2025, 42: msaf131. PMID: 40452442, PMCID: PMC12203517, DOI: 10.1093/molbev/msaf131.Peer-Reviewed Original ResearchConceptsRate of gene expression evolutionGene expression evolutionExpression evolutionGene expressionPhenotypic evolutionHeterogeneous rates of evolutionNonsynonymous to synonymous substitution ratesRates of phenotypic evolutionDevelopmental stagesSingle-copy orthologsGene sequence evolutionSynonymous substitution ratesRate of evolutionExpression of genesFunctional pathway analysisCarbon metabolismEvolutionary forcesConsequent phenotypesSexual reproductionSequence evolutionConserved pathwaysMeiosis pathwaysSubstitution ratesCell cyclePathway analysis
2024
Evolutionary Innovations in Conserved Regulatory Elements Associate With Developmental Genes in Mammals
Uebbing S, Kocher A, Baumgartner M, Ji Y, Bai S, Xing X, Nottoli T, Noonan J. Evolutionary Innovations in Conserved Regulatory Elements Associate With Developmental Genes in Mammals. Molecular Biology And Evolution 2024, 41: msae199. PMID: 39302728, PMCID: PMC11465374, DOI: 10.1093/molbev/msae199.Peer-Reviewed Original ResearchSequence evolutionRegulatory evolutionDevelopmental signaling genesEnhanced evolutionEvolutionary innovationMammalian phylogenyTranscriptional enhancersGenetic variationPhenotypic variationPleiotropic genesDevelopmental genesEnhancer elementsHoofed mammalsEnhancer sequencesActivation domainSignaling GenesEvolutionary adaptationDiverse organismsGenesHuman diseasesRegulatory functionsDevelopmental processesDeveloping limbCell typesMammals
2009
Short-Term Signatures of Evolutionary Change in the Salmonella enterica Serovar Typhimurium 14028 Genome
Jarvik T, Smillie C, Groisman EA, Ochman H. Short-Term Signatures of Evolutionary Change in the Salmonella enterica Serovar Typhimurium 14028 Genome. Journal Of Bacteriology 2009, 192: 560-567. PMID: 19897643, PMCID: PMC2805332, DOI: 10.1128/jb.01233-09.Peer-Reviewed Original ResearchConceptsComplete genomic sequenceGenomic sequencesSalmonella enterica serovar TyphimuriumTyphoid-like diseaseEnterica serovar TyphimuriumEvolutionary changeSequence evolutionGram-negative pathogensS. typhimuriumSerovar TyphimuriumComplete inventoryGenetic alterationsAvirulent strainsS. entericaPathogenic organismsSequenceLaboratory passageS. typhimurium strainTyphimuriumGenomeStrainsTyphimurium strainsLT2 strainOrganismsProgenitorsMeasuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies
Otto W, Stadler PF, López-Giraldéz F, Townsend JP, Lynch VJ, Wagner GP. Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies. Genome Biology And Evolution 2009, 1: 85-98. PMID: 20333180, PMCID: PMC2817405, DOI: 10.1093/gbe/evp010.Peer-Reviewed Original ResearchTranscription factor-binding sitesCis-regulatory elementsHOXA clusterSelective pressureGene expression evolutionMethionine biosynthesis pathwayLow sequence similarityFactor-binding sitesClade-specific differencesTurnover rateExpression evolutionSpecies treeBiosynthesis pathwayRelated speciesSequence similaritySite turnoverDifferent organismsSequence evolutionTranscription factorsDifferent cladesFungal dataProgesterone response elementMaximum likelihood modelVertebratesTurnover
2006
Identifying the Fundamental Units of Diversity Among Bacillus Isolates From "Evolution Canyon" III
Perry E, Koeppel A, Krizanc D, Rooney A, Sikorski J, Nevo E, Cohan F. Identifying the Fundamental Units of Diversity Among Bacillus Isolates From "Evolution Canyon" III. Israel Journal Of Ecology And Evolution 2006, 52: 543-552. DOI: 10.1560/ijee_52_3-4_543.Peer-Reviewed Original ResearchBacterial systematicsEvolution CanyonDistinct populationsSequence diversity patternsDNA sequence diversityLineage-specific ratesSingle bacterial speciesEcological distinctnessFundamental unitPutative ecotypesMicrobial ecologistsDiversity patternsDistinct lineagesEcological diversityDifferent microhabitatsSequence evolutionSequence dataSequence diversityBacterial diversityCladeSequence clustersBacterial speciesBacillus subtilisBacillus isolatesEvolutionary simulations
2002
The evolutionary origin of Indian Ocean tortoises (Dipsochelys)
Palkovacs E, Gerlach J, Caccone A. The evolutionary origin of Indian Ocean tortoises (Dipsochelys). Molecular Phylogenetics And Evolution 2002, 24: 216-227. PMID: 12144758, DOI: 10.1016/s1055-7903(02)00211-7.Peer-Reviewed Original ResearchConceptsWestern Indian Ocean islandsGiant tortoisesIndian Ocean islandsIndian Ocean giant tortoisesIndian OceanCyt b geneDNA substitution ratesOcean islandsShort generation timeSmall body sizeSource of colonizationMalagasy lineagesEvolutionary originWestern Indian OceanWild populationsMitochondrial DNAPhylogenetic analysisSequence evolutionB geneSubstitution ratesBody sizeOcean currentsEast coastGeneration timeTortoises
2000
Evolution of Hoxa-11 in Lineages Phylogenetically Positioned along the Fin–Limb Transition
Chiu C, Nonaka D, Xue L, Amemiya C, Wagner G. Evolution of Hoxa-11 in Lineages Phylogenetically Positioned along the Fin–Limb Transition. Molecular Phylogenetics And Evolution 2000, 17: 305-316. PMID: 11083943, DOI: 10.1006/mpev.2000.0837.Peer-Reviewed Original ResearchMeSH KeywordsAlanineAmino Acid SequenceAnimalsBinding SitesCell LineConserved SequenceDNAEvolution, MolecularExtremitiesFishesHeLa CellsHomeodomain ProteinsHumansIntronsMolecular Sequence DataPhylogenyProtein IsoformsSequence AlignmentSequence Analysis, DNASequence Homology, Amino AcidXenopusXenopus ProteinsZebrafishZebrafish ProteinsConceptsFin-limb transitionSequence evolutionAmino acid sequence comparisonsHoxa-11Domain IElectrophoretic mobility shift assaysMobility shift assaysAmino acid sequencePatterns of evolutionConsecutive alanine residuesWhole cell extractsEvolutionary timeAppendage developmentCharacter reconstructionEvolutionary changeTranscription factorsSequence comparisonIntron sequencesNucleotide conservationShift assaysAcid sequenceAlanine residuesLineagesAccelerated rateCoelacanth
1986
Functional complementation between mutations in a yeast suppressor tRNA gene reveals potential for evolution of tRNA sequences.
Willis I, Nichols M, Chisholm V, Söll D, Heyer W, Szankasi P, Amstutz H, Munz P, Kohli J. Functional complementation between mutations in a yeast suppressor tRNA gene reveals potential for evolution of tRNA sequences. Proceedings Of The National Academy Of Sciences Of The United States Of America 1986, 83: 7860-7864. PMID: 3532123, PMCID: PMC386822, DOI: 10.1073/pnas.83.20.7860.Peer-Reviewed Original ResearchConceptsMutant tRNA precursorS. pombe genesSuppressor tRNA geneNucleotide sequence evolutionRNA processing levelRNase P cleavagePombe geneTRNA genesFunctional complementationComplementation eventsS. pombeCycle of inactivationTRNA sequencesTRNA precursorsSequence evolutionSaccharomyces cerevisiaeS. cerevisiaePombe strainSchizosaccharomyces pombe strainStructural domainsDifferential expressionSuppressor functionP cleavageGenesSuppressor
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